Summary of my professional life

David Jimenez-Morales

PhD, MSc, BSc

Why am I doing Science?

EDUCATION

2006 - 2013

PhD Bioinformatics

Department of Bioengineering. University of Illinois at Chicago. Chicago, Illinois (USA)

2003 - 2004

MSc Computational Biology

Universidad Complutense de Madrid. Madrid (Spain)

1999

Teaching Certificate (Postgraduate Certificate in Education)

Instituto de Ciencias de la Educación. Universidad Complutense de Madrid. Madrid (Spain)

1998 - 2000

Microbiology PhD Program and Research Certificate

Department of Microbiology I, Universidad Complusense de Madrid.

1993 - 1998

BSc Biology

Facultad de Ciencias. Universidad de Granada. Granada (Spain)

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EXPERIENCE

2021 -

Senior Research Engineer (Academic Staff Research)

2018 - 2020. Senior Computational Biologist (Staff Scientist)

The Ashley lab. Department of Medicine, Division of Cardiovascular Medicine. Stanford University

2015 - 2018

Researcher (Staff Scientist)

The Krogan lab. Department of Cellular and Molecular Pharmacology (CMP). University of California San Francisco (UCSF)

2016 - 2018

Visiting Scientist

Gladstone Institutes. San Francisco, CA

2013 - 2018

Bioengineering Department Affiliate

Department of Bioengineering. University of Illinois-Chicago. Chicago

2014 - 2015

Research Associate (Software Developer and Bioinformatics Specialist)

dictyBase.org. Center for Genetic Medicine. Northwestern University. Chicago

2013 - 2015

Visiting Research Associate

Shannon Hackett's lab. Bird Division. The Field Museum of Natural History. Chicago

2013 - 2014

Visiting Instructor

Prof Bob Eisenberg’s Lab. Department of Molecular. Biophysics & Physiology. Rush University Medical Center. Chicago.

2006 - 2013

PhD Graduate Student

Jie Liang’s Molecular and Systems Computational lab. Department of Bioengineering. University of Illinois-Chicago. Chicago

2003 - 2005

Research Assistant

Proteomics Unit & Department of Microbiology II. Universidad Complutense de Madrid – Parque Científico de Madrid. Madrid

1998 - 2000

Research Assistant

Department of Microbiology I. Faculty of Medicine. Universidad Complutense de Madrid. Madrid.

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PUBLICATIONS

Peer-reviewed Journals n = 26

2021 - Malene E Lindholm, David Jimenez-Morales, Han Zhu, Kinya Seo, David Amar, Chunli Zhao, Archana Raja, Roshni Madhvani, Sarah Abramowitz, Cedric Espenel, Shirley Sutton, Colleen Caleshu, Gerald J Berry, Kara S Motonaga, Kyla Dunn, Julia Platt, Euan A Ashley, Matthew T Wheeler

Mono- and Biallelic Protein-Truncating Variants in Alpha-Actinin 2 Cause Cardiomyopathy Through Distinct Mechanisms

Circ Genom Precis Med. 2021 Nov 22. doi: 10.1161/CIRCGEN.121.003419

2021 - Danielle L. Swaney, Dana J. Ramms, Zhiyong Wang, Jisoo Park, Yusuke Goto, Margaret Soucheray, Neil Bhola, Kyumin Kim, Fan Zheng, Yan Zeng, Michael McGregor, Kari A. Herrington, Rachel O’Keefe, Nan Jin, Nathan K. VanLandingham, Helene Foussard, John Von Dollen, Mehdi Bouhaddou, David Jimenez-Morales, Kirsten Obernier, Jason F. Kreisberg, Minkyu Kim, Daniel E. Johnson, Natalia Jura, Jennifer R. Grandis, J. Silvio Gutkind, Trey Ideker, Nevan J. Krogan

A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity

Science. Oct 1, 2021. doi: 10.1126/science.abf2911

2021 - Laura Martin-Sancho, Shashank Tripathi, Ariel Rodriguez-Frandsen, Lars Pache, Maite Sanchez-Aparicio, Michael J. McGregor, Kelsey M. Haas, Danielle L. Swaney, Thong T. Nguyen, Joao I. Mamede, Christopher Churas, Dexter Pratt, Sara B. Rosenthal, Laura Riva, Courtney Nguyen, Nish Beltran-Raygoza, Stephen Soonthornvacharin, Guojun Wang, David Jimenez-Morales, Paul D. De Jesus, Hong M. Moulton, David A. Stein, Max W. Chang, Chris Benner, Trey Ideker, Randy A. Albrecht, Judd F. Hultquist, Nevan J. Krogan, Adolfo García-Sastre & Sumit K. Chanda

Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy

Nature Microbiology. Sept 23, 2021. doi: 10.1038/s41564-021-00964-2

2021 - Esther Paulo, Yun Zhang, Ruchi Masand, Tony L. Huynh, Youngho Seo, Danielle L. Swaney, Margaret Soucheray, Erica Stevenson, David Jimenez-Morales, Nevan J. Krogan, Biao Wang

Brown adipocyte ATF4 activation improves thermoregulation and systemic metabolism

Cell Reports. Vol 36, Issue 12, 109742, Sept 21, 2021. doi: 10.1016/j.celrep.2021.109742

2021 - COVID-19 Host Genetics Initiative

Mapping the human genetic architecture of COVID-19

Nature. 2021 Jul 8. doi: 10.1038/s41586-021-03767-x

2021 - Nikoleta G Tsvetanova, Michelle Trester-Zedlitz, Billy W Newton, Grace E Peng, Jeffrey R Johnson, David Jimenez-Morales, Andrew P Kurland, Nevan J Krogan, Mark von Zastrow

Endosomal cAMP production broadly impacts the cellular phosphoproteome

J Biol Chem. 2021 Jun 21;100907. doi: 10.1016/j.jbc.2021.100907

2021 - Aaron J. Wilk, Madeline J. Lee, Bei Wei, Benjamin Parks, Ruoxi Pi, Giovanny J. Martínez-Colón, Thanmayi Ranganath, Nancy Q. Zhao, Shalina Taylor, Winston Becker, Stanford COVID-19 Biobank, David Jimenez-Morales, Andra L. Blomkalns, Ruth O’Hara, Euan A. Ashley, Kari C. Nadeau, Samuel Yang, Susan Holmes, Marlene Rabinovitch, Angela J. Rogers, William J. Greenleaf, Catherine A. Blish

Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19

J Exp Med. (2021) 218 (8): e20210582. doi: 10.1084/jem.20210582

2020 - The Molecular Transducers of Physical Activity Consortium

Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise

Cell. Volume 181, Issue 7, P1464-1474, June 25, 2020. doi: 10.1016/j.cell.2020.06.004

2020 - Jonathan M Budzik, Danielle L Swaney, David Jimenez-Morales, Jeffrey R Johnson, Nicholas E Garelis, Teresa Repasy, Allison W Roberts, Lauren M Popov, Trevor J Parry, Dexter Pratt, Trey Ideker, Nevan J Krogan, Jeffery S Cox

Dynamic post-translational modification profiling of M. tuberculosis-infected primary macrophages

eLife. 2020;9:e51461. doi: 10.7554/eLife.51461 . Datasets assembled into an on-line application: TB OMICS EXPLORER

2019 - Jeng EE, Bhadkamkar V, Ibe NU, Gause H, Jiang L, Chan J, Jian R, Jimenez-Morales D, Stevenson E, Krogan NJ, Swaney DL, Snyder MP, Mukherjee S, Bassik MC.

Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen

Cell Host Microbe.. 2019 Sep 10. pii: S1931-3128(19)30426-3. doi: 10.1016/j.chom.2019.08.017

2019 - Adam L. Orra, Chaeyoung Kima, David Jimenez-Morales, Billy W. Newton, Jeffrey R. Johnson, Nevan J. Krogan, Danielle L. Swaney, and Robert W. Mahley

Neuronal Apolipoprotein E4 Expression Results in Proteome-Wide Alterations and Compromises Bioenergetic Capacity by Disrupting Mitochondrial Function

Journal of Alzheimer's Disease. 2019;68(3):991-1011. doi: 10.3233/JAD-181184

2018 - L. Bramasole, A. Sinha, S. Gurevich, M. Radzinski, Y. Klein, N. Panat, E. Gefen, T. Rinaldi, D. Jimenez-Morales, J. Johnson, N.J. Krogan, N. Reis, D. Reichmann, M.H. Glickman, E. Pick

Proteasome Lid Bridges Mitochondrial Stress with Cdc53/Cullin1 NEDDylation Status

Redox Biol. 2018 Nov 17; 20:533-543

2018 - Krystal A Fontaine, Kristoffer E Leon, Mir Mubashir Khalid, David Jimenez-Morales, Julia Kaye, Priya Shah, Steven Finkbeiner, Nevan Krogan, Melanie Ott

The cellular NMD pathway restricts Zika virus infection and is targeted by the viral capsid protein

MBio. 2018 Nov 06; 9(6). Pre-printed at bioRxiv.

2018 - Nan Zhao, Vittorio Sebastiano, Natasha Moshkina, Nacho Mena, Judd Hultquist, David Jimenez-Morales, Yixuan Ma, Alexander Rialdi, Randy Albrecht, Romain Fenouil, Maria Teresa Sanchez-Aparicio, Juan Ayllon, Sweta Ravisankar, Bahareh Haddad, Jessica Sook Yuin Ho, Diana Low, Jian Jin, Yurchenko Vyacheslav, Rabinder Prinjha, Alexander Tarakhovsky, Massimo Squatrito, Dalila Pinto, Allette Kimaada, Minji Byun, Melissa Smith, Robert Sebra, Ernesto Guccione, Terrence Tumpey, Nevan Krogan, Harm van Bakel, Benjamin Greenbaum, Adolfo Garcia-Sastre, and Ivan Marazzi

Influenza virus infection causes global RNAPII termination defects

Nature Structural & Molecular Biology. 2018 Sep;25(9):885-893. doi: 10.1038/s41594-018-0124-7. Epub 2018 Sep 3.

2018 - Esther Paulo, Dongmei Wu, Yangmeng Wang, Yun Zhang, Yixuan Wu, Danielle L. Swaney, Margaret Soucheray, David Jimenez-Morales, Ajay Chawla, Nevan J. Krogan & Biao Wang

Sympathetic inputs regulate adaptive thermogenesis in brown adipose tissue through cAMP-Salt inducible kinase axis.

Sci Rep. 2018 Jul 20; 8(1):11001

2018 - Kristin L. Patrick, Jason A. Wojcechowskyj, Tao Jing, Morgan Riba, Sara Talmage, Pengbiao Xu, Samantha L. Bell, Ana L. Cabello, Jiewei Xu, Michael Shales, David Jimenez-Morales, Thomas A. Ficht, Paul de Figueiredo, James E. Samuel1, Pingwei Li, Nevan J. Krogan, Robert O. Watson

Quantitative yeast genetic interaction profiling of bacterial effector proteins uncovers a role for the human retromer in Salmonella infection

Cell Syst. 2018 Jul 26.

2018 - Ruchi Masand, Esther Paulo, Dongmei Wu , Yangmeng Wang, Danielle L. Swaney, David Jimenez-Morales, Nevan J. Krogan, and Biao Wang

Proteome Imbalance of Mitochondrial Electron Transport Chain in Brown Adipocytes Leads to Metabolic Benefits.

Cell Metab. 2018 Mar 06; 27(3):616-629.e4

2017 - Rialdi A, Hultquist J, Jimenez-Morales D, Peralta Z, Campisi L, Fenouil R, Moshkina N, Wang Zhen Z, Laffleur B, Michael R, Haas K, Pefanis E, Albrecht A. R, Jen J, Basu U, Garcia-Sastre A, van Bakel H, Krogan N, Marazzi I

The RNA Exosome Syncs IAV-RNAPII Transcription to Promote Viral Ribogenesis and Infectivity.

Cell 2017 May 4;169(4):679-692.e14.

2015 - Basu S, Fey P, Jimenez-Morales D, Dodson RJ, Chisholm RL

dictyBase 2015: Expanding data and annotations in a new software environment.

Genesis 2015 Jun 19.

2014 - Jimenez-Morales D, Adamian L, Shi D, and Liang J.

Lysine Carboxylation: Unveiling a spontaneous posttranslational modification.

Acta Crystallogr D Biol Crystallogr. 2014 Jan;70(Pt 1):48-57

> Supplementary information and PreLysCar.

2012 - Jimenez-Morales D, Liang J, and Eisenberg B.

Ionizable Side Chains at Catalytic Active Sites of Enzymes.

Eur Biophys J. Vol 41, Issue 5 (2012), P 449-460.

2012 - Naveed H, Jimenez-Morales D, Tian J, Pasupuleti V, Kenney L, Liang L (2012).

Engineered oligomerization state of OmpF protein through computational design decouples oligomer dissociation from unfolding.

J Mol Biol. 2012 May 25;419(1-2):89-101.

2011 - Liang J, Naveed H, Jimenez-Morales D, Adamian L, Lin M.

Computational studies of membrane proteins: Models and predictions for biological understanding.

Biochim Biophys Acta. 2011 Oct 12.

2011 - Jimenez-Morales D and Liang J.

Pattern of Amino Acid Substitutions in Transmembrane Domains of β-Barrel Membrane Proteins for Detecting Remote Homologs in Bacteria and Mitochondria.

PLoS ONE. 2011;6(11):e26400. Epub 2011 Nov 1.

Supplementary information and bbTM-SearchTool.

2008 - Jimenez-Morales D, Adamian L, and Liang J.

Detecting Remote Homologues Using Scoring Matrices Calculated from the Estimation of Amino Acid Substitution Rates of Beta-Barrel Membrane Proteins.

Conf Proc IEEE Eng Med Biol Soc. 2008, 30:1347-1350.

2008 - Jimenez-Morales D.

Substitution Rates of Amino Acid residues in Transmembrane Regions of Beta-Barrel Membrane Proteins.

BioE Student Journal. N1, 2008. Front Cover.

Books

2001 - Coauthor.

Propiedades adicionales no antibióticas de los macrólidos.

Scientific Communication Management Editors.

2001 - Coauthor.

Guía Setas Autóctonas.

Editorial Doyma. Madrid.

Popular Science Articles

2000 - Jimenez-Morales D.

Problematic in the use of antiobiotics in animal farms.

Nº41. Ganaderos Magazine. sp

2000 - Jimenez-Morales D.

Bovine spongiform encephalopathy.

Nº37. Ganaderos Magazine.

Abstracts & Communications

2019 - David Jimenez-Morales

artMS: Analytical R Tools for Mass Spectrometry (Link to slides)

2019 SUMS-RAS (Stanford University Mass Spectrometry - Research Application Symposium). Stanford, CA

2019 - David Jimenez-Morales, David Jimenez-Morales; John Von Dollen; Alexandre Rosa Campos; Nevan J Krogan; Danielle Swaney

artMS: Analytical R Tools for Mass Spectrometry

67th Annual Conference American Society for Mass Spectrometry (ASMS) Conference on Mass Spectrometry and Allied Topicds. 2019 Atlanta, Georgia

2017 - David Jimenez-Morales, Judd Hultquist, John Von Dollen, Jeff Johnson, Hannes Braberg, and Nevan J Krogan

Influenza virus networks of pathogenesis inferred from the integration of multiple large-scale datasets.

Annual Programmatic Meeting. NIAID-NIH, Systems Biology for Infectious Diseases (SBID) Research. May 7-10, 2017 Chicago, IL.

2017 - Kelsey Haas, Michael McGregor, David Jimenez-Morales, Judd Hultquist and Nevan Krogan

Destroying the “Non-self”: Defining Influenza A Viral Endonuclease Mechanisms for Host Shutoff.

Annual Programmatic Meeting. NIAID-NIH, Systems Biology for Infectious Diseases (SBID) Research. May 7-10, 2017 Chicago, IL.

2017 - Judd F. Hultquist, David Jimenez-Morales, Michael M. McGregor, Kelsey Haas, Jeffrey Johnson, William Newton, Giorgi Metreveli, Matthew Urbanowski, Megan Shaw, Ivan Marazzi, Randy A. Albrecht, Adolfo Garcia-Sastre, and Nevan J. Krogan

Proteomic Profiling of Influenza A Virus Infection Reveals Strain-specific Rewiring of Host Cell Networks.

Annual Programmatic Meeting. NIAID-NIH, Systems Biology for Infectious Diseases (SBID) Research. May 7-10, 2017 Chicago, IL.

2017 - Celina Cahalane, David Jimenez-Morales, John VonDollen, Hannah Baumann, Matthew Urbanowksi, Megan Shaw, Giorgi Metreveli, Nevan Krogan, Adolfo Garcia-Sastre, Oswald Quehenberger, Edward Dennis, and Leah Shriver

Metabolic Profiling of Influenza Infection.

Annual Programmatic Meeting. NIAID-NIH, Systems Biology for Infectious Diseases (SBID) Research. May 7-10, 2017 Chicago, IL.

2016 - Jimenez-Morales D, Von Dollen J, Braberg H, Verschueren E, and Krogan NJ.

Predictive models for the identification of networks involved in host responses to influenza virus infection.

2nd Annual Host- Pathogen Interactions: Circuits to Systems Symposium. Jan 4, 2016. San Diego, CA.

2011 - Jimenez-Morales D, Liang J, and Eisenberg B.

Active Sites of Enzymes are Crowded with Charge.

Biophysical Journal. 100(3): p. 218a. Abstract 1191-Pos and Poster Board B101.

2011 - Jimenez-Morales D, Liang J, and Eisenberg B.

Active Sites of Enzymes are Crowded with Charge.

6th Annual Midwest Conference on Protein Folding, Assembly, and Molecular Motions. University of Notre Dame.

2010 - Jimenez-Morales D, Li R, Wang Z, Li Y, Liu L, Liang J.

Evolutionary Speed of Enzymes Functional Surfaces and their Relationship with Metabolic Fluxes in Networks of Central Carbon Metabolism of Bacteria.

Biophysical Journal 98(3) pp. 741a

2008 - Jimenez-Morales D, Adamian L, Liang J.

Substitution Rates Of Amino Acid Residues In Transmembrane - Extracellular And Periplasmic- Regions Of Beta-Barrel Membrane Proteins.

Biophysical Journal 94(2) pp. 1959

2002 - Jimenez-Morales D.

Tools for the Apored Virtual.

V-Aporeunión. Tordesillas (Valladolid). Oral presentation: I introduced the improvements in the new Apoweb.

1999 - Jimenez-Morales D, Heredia S, Calvo A, Gomez-Luz ML, Prieto J.

Sensibilidad a antimicrobianos de Enterococcus faecalis de procedencia animal.

Spanish Chemotherapy Society Congress. May 1999

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TEACHING

Workshop Instructor

Association of Biomolecular Resource Facilities (ABRF)

March 2021 - Using R in Proteomics Core: from QC to Data Analysis. Slides

Courses as Instructor

Department of Bioengineering. University of Illinois at Chicago.

Fall 2010 - BIOE480: Introduction to Bioinformatics.

Fall 2012 - BIOE481: Bioinformatics Laboratory.

Courses as Teaching Assistant

Department of Bioengineering. University of Illinois at Chicago.

Spring 2013 - BIOE250, Clinical Problems in Bioengineering.

Fall 2012 - BIOE481: Bioinformatics Laboratory.

Fall 2010, 2012 - BIOE480, Introduction to Bioinformatics.

Spring 2007 - BIOE455, Intro to Cell and Tissue Engineering.

Fall 2006 - BIOE240, Modeling Physiological Data & Systems

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COMPUTING

Bioinformatics Tools

I have developed the following tools:

R package: artMS: Analytical R Tools for Mass Spectrometry. Check the Github repo and the Bioconductor page.

R package: MotrpacBicQC: Primary and Secondary QC/QA analysis of datasets generated by the Metabolomic and Proteomic Chemical Analysis Sites (CAS) of the Molecular Transducer of Physical Activity Consortium (MoTrPAC)

bioNeNa (the FluOMICS bioNetwork Navigator): a systems biology tool to explore large-scale datasets

TB OMICS EXPLORER: Multi-OMICS profiling of primary macrophages during Mycobacterium tuberculosis (TB) infection (part of this publication)

MIDTOD: Metabolite Identification Through Orthogonal Datasets (under development).

PreLysCar (Predictor of Lysine Carboxylation), also available as a tool in the suite of structural biology programs CCP4

bbTM-ST (beta-barrel TransMembrane Search Tool).

Skills

Operating Systems: Unix/Linux and Mac OS X. Virtual Computing: Docker, Vagrant.

Bioinformatics Packages. Sequence analysis software (Blast, MEME-MAST, ClustalW, T-Coffee, HMMER, HHsearch,...); Molecular structures visualization software (PyMOL, VMD, Rasmol, Dino, SPDBV); Molecular dynamics (NAMD); Molecular interactions (Mint, Osprey); Genomics: Maker, FastQC, ALLPATHS-LG, Circos, GeneMark, QIIME, Galaxy; etc

Programming languages: R (also Shiny), Python, Perl, Unix shell scripts, HTML, CSS (Bootstrap), Javascript (AngularJS, Node.js), Ruby on Rails, PHP, Matlab, C/C++, Java.

Databases: Relational: PostgreSQL & MySQL. SQL language. Generic Model Organism Database Chado schema of relational databases. NoSQL databases: Neo4j. Search engine: elasticsearch

GMOD tools: JBrowse, WebApollo, InterMine.

Others: Source code management (git/github); Design (Photoshop); Statistician (R, SAS, SPSS).

Web Design and Development

2017 - Krogan Lab. UCSF. San Francisco, CA (USA)

2016 - FluOMICS. UCSF. San Francisco, CA (USA)

2016 - New Dictybase. Dictybase. Northwestern University. Chicago (IL, USA)

2015 - dictyMeeting 2015. Dictybase. Northwestern University. Chicago (IL, USA)

2003 - Proteomic Unit. Facultad de Farmacia. UCM-PCM (Madrid, Spain)

2002, 2005 - Spanish Network of Apoptosis (APORED) Department of Cell and Developmental Biology. Centro de Investigaciones Biológicas (CIB-CSIC)

Software Administration

2002 - 2005 - Spanish Network of Apoptosis (APORED). Department of Cell and Developmental Biology. CIB-CSIC. Administrator of workspace BSCW (Basic Support for Cooperative Work) of the APORED. List co-administrator of APORED email distribution list, and list administrator of Apobecarios email distribution list. Website updates

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AWARDS

U19AI135972: “FluOMICS, The Next Generation”.

2018 – 2022. Co-PI Modeling Core. Co-PI Data Management and Bioinformatics Core (DMBC). NIH/NIAID

Pilot Project (U19AI106754): “Development of a web-based computational tool for integrating and navigating systems biology data and models”.

2017 – 2018. Principal Investigator. NIH/NIAID

Beca Talentia Excellence Grant

2008 - 2010. Regional Ministry for Innovation, Science and Enterprise. Junta de Andalucía. Spain.

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LINKS

Videos

Learn how soap stops the coronavirus (by Sarartistic)

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